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- PDB-5cdo: 3.15A structure of QPT-1 with S.aureus DNA gyrase and DNA -

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Basic information

Entry
Database: PDB / ID: 5cdo
Title3.15A structure of QPT-1 with S.aureus DNA gyrase and DNA
Components
  • (DNA gyrase subunit ...) x 2
  • DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE / ANTIBACTERIAL / INHIBITOR
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rossmann fold - #670 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily ...Rossmann fold - #670 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-50M / Chem-53L / Chem-53M / : / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.15 Å
AuthorsBax, B.D. / Srikannathasan, V. / Chan, P.F.
Citation
Journal: Nat Commun / Year: 2015
Title: Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin.
Authors: Chan, P.F. / Srikannathasan, V. / Huang, J. / Cui, H. / Fosberry, A.P. / Gu, M. / Hann, M.M. / Hibbs, M. / Homes, P. / Ingraham, K. / Pizzollo, J. / Shen, C. / Shillings, A.J. / Spitzfaden, ...Authors: Chan, P.F. / Srikannathasan, V. / Huang, J. / Cui, H. / Fosberry, A.P. / Gu, M. / Hann, M.M. / Hibbs, M. / Homes, P. / Ingraham, K. / Pizzollo, J. / Shen, C. / Shillings, A.J. / Spitzfaden, C.E. / Tanner, R. / Theobald, A.J. / Stavenger, R.A. / Bax, B.D. / Gwynn, M.N.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Crystallization and initial crystallographic analysis of covalent DNA-cleavage complexes of Staphyloccocus aureus DNA gyrase with QPT-1, moxifloxacin and etoposide.
Authors: Srikannathasan, V. / Wohlkonig, A. / Shillings, A. / Singh, O. / Chan, P.F. / Huang, J. / Gwynn, M.N. / Fosberry, A.P. / Homes, P. / Hibbs, M. / Theobald, A.J. / Spitzfaden, C. / Bax, B.D.
History
DepositionJul 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase subunit A
B: DNA gyrase subunit B,DNA gyrase subunit B
C: DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B
E: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
F: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
R: DNA gyrase subunit A
S: DNA gyrase subunit B,DNA gyrase subunit B
T: DNA gyrase subunit A
U: DNA gyrase subunit B,DNA gyrase subunit B
V: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
W: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,73833
Polymers328,15712
Non-polymers2,58121
Water1,47782
1
A: DNA gyrase subunit A
B: DNA gyrase subunit B,DNA gyrase subunit B
C: DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B
E: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
F: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,37917
Polymers164,0796
Non-polymers1,30011
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
R: DNA gyrase subunit A
S: DNA gyrase subunit B,DNA gyrase subunit B
T: DNA gyrase subunit A
U: DNA gyrase subunit B,DNA gyrase subunit B
V: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
W: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,36016
Polymers164,0796
Non-polymers1,28110
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.472, 170.211, 124.579
Angle α, β, γ (deg.)90.000, 102.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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DNA gyrase subunit ... , 2 types, 8 molecules ACRTBDSU

#1: Protein
DNA gyrase subunit A /


Mass: 54777.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XG5, EC: 5.99.1.3
#2: Protein
DNA gyrase subunit B,DNA gyrase subunit B /


Mass: 21111.018 Da / Num. of mol.: 4 / Fragment: residues 417-638,residues 417-638
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: gyrB, SA0005 / Production host: Escherichia coli (E. coli) / References: UniProt: P66937, EC: 5.99.1.3

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DNA chain , 1 types, 4 molecules EFVW

#3: DNA chain
DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')


Mass: 6150.966 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 8 types, 103 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Source: (synth.) synthetic construct (others)
#8: Chemical ChemComp-53M / (2R,4S,4aS)-4',6'-dihydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidin]-2'-one


Mass: 374.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N4O6
#9: Chemical ChemComp-53L / (2R,4S,4aS,5S)-6'-hydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4'(3'H)-dione


Mass: 374.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N4O6
#10: Chemical ChemComp-50M / (2R,4S,4aS,5R)-6'-hydroxy-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4'(3'H)-dione


Mass: 374.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N4O6
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.2 / Details: 150mM BisTris pH6.2, 11% PEG 5000 MME / PH range: 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97627 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
20.976271
ReflectionResolution: 3.15→58.42 Å / Num. obs: 62354 / % possible obs: 98.2 % / Redundancy: 3 % / Biso Wilson estimate: 48.78 Å2 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.087 / Net I/σ(I): 7.7 / Num. measured all: 185026
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
3.15-3.2630.4142.81847261750.28698.7
12.2-58.422.90.06215.4315410780.04394.9

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Processing

Software
NameVersionClassification
Aimless3.3.16data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementResolution: 3.15→58.415 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 2510 4.03 %
Rwork0.2151 59797 -
obs0.2163 62307 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.38 Å2 / Biso mean: 50.3513 Å2 / Biso min: 8.99 Å2
Refinement stepCycle: final / Resolution: 3.15→58.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20865 1597 274 82 22818
Biso mean--31.29 30.75 -
Num. residues----2751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523130
X-RAY DIFFRACTIONf_angle_d0.97231595
X-RAY DIFFRACTIONf_chiral_restr0.0633581
X-RAY DIFFRACTIONf_plane_restr0.0043893
X-RAY DIFFRACTIONf_dihedral_angle_d18.068858
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.15-3.21060.33511360.29623362349899
3.2106-3.27610.34761340.2823305343998
3.2761-3.34730.30061320.26293335346798
3.3473-3.42520.27131470.25943303345098
3.4252-3.51080.30141470.24713293344097
3.5108-3.60580.24571380.22573336347499
3.6058-3.71180.29891400.22583331347198
3.7118-3.83160.21961410.21623343348499
3.8316-3.96850.24991330.21243303343698
3.9685-4.12740.25741370.19743355349299
4.1274-4.31520.21191490.19263297344698
4.3152-4.54260.23161430.18353291343497
4.5426-4.82710.21811450.183315346098
4.8271-5.19960.21091300.18893354348498
5.1996-5.72240.23311420.20613331347398
5.7224-6.54950.24141260.21733310343697
6.5495-8.2480.24631520.213307345997
8.248-58.42530.20371380.20583326346496
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5636-0.07680.01040.56710.05150.34010.0032-0.00250.1484-0.12170.00990.15020.046-0.0904-0.01730.2234-0.0389-0.02860.2799-0.01580.366435.4346-30.669755.1404
21.7507-0.23330.37991.0349-0.21682.10350.3601-0.3944-0.46940.6147-0.1512-0.28130.53980.2838-0.16240.4766-0.0122-0.11510.52340.1030.396641.3698-50.775983.7504
31.9179-0.0493-0.1412.41520.0861.9929-0.23330.1537-0.423-0.5620.0649-0.10210.5494-0.29510.13270.5267-0.17630.03090.4177-0.00730.369727.9003-52.487133.5457
42.49090.9289-0.01742.21110.24951.2493-0.05060.05410.1390.12570.21320.259-0.0804-0.0019-0.10670.30020.0312-0.020.3068-0.03020.479945.620916.951562.6068
52.3140.02841.13541.40810.47012.3393-0.0796-0.5023-0.21340.25010.23520.54660.0393-0.6717-0.17270.2209-0.15180.02390.56160.04540.495922.5972-42.427880.6624
60.61910.0835-0.13022.8320.3491.14230.0458-0.02340.2137-0.1856-0.0715-0.2085-0.2662-0.03430.02330.18580.0707-0.0110.2138-0.03530.388377.9338-27.152968.725
71.35250.00870.42481.29410.05030.93660.11710.3717-0.2038-0.581-0.04690.3105-0.1134-0.3065-0.07640.59170.1399-0.05350.52-0.02030.329962.8217-52.367338.1463
82.2358-0.99680.38161.9638-0.90481.77660.00660.19810.25-0.1853-0.0836-0.2836-0.21380.0755-0.04260.3349-0.05880.06770.2167-0.02470.356366.258416.777359.5224
91.9228-0.10580.26242.0527-0.27092.4983-0.1189-0.0798-0.52250.22190.10840.16420.48950.13260.03480.35780.10350.03910.42950.03270.365775.5725-55.424288.6761
102.5805-0.1259-0.81773.92620.18752.0048-0.12030.39060.0647-0.55360.2171-0.57220.02750.1477-0.05130.53710.09160.09260.4323-0.0170.464682.8628-46.82441.6012
111.9227-0.5671-0.24970.36030.08240.48150.04310.17280.3405-0.0465-0.0207-0.0748-0.18760.113-0.03440.2367-0.0630.00850.24060.03420.322487.151-28.0829-5.6642
121.2247-0.18130.29131.04790.2391.52570.2434-0.37280.59570.5413-0.11440.4912-0.466-0.22010.00360.72-0.03690.20390.4437-0.11350.492579.6406-7.3421.6146
132.89090.9014-0.1651.7516-0.20670.7951-0.0831-0.0235-0.3636-0.16390.07660.07170.0551-0.02620.10340.4052-0.0090.07260.26480.07360.582275.7093-76.00432.9549
141.14530.3305-0.28092.5536-0.83441.38150.05440.61111.0659-1.0647-0.2836-0.5391-0.7066-0.00310.22790.6366-0.3-0.04420.72380.52621.082195.7767-7.7664-28.0962
151.6378-0.26380.11591.45880.02522.51160.0822-0.82660.74280.8148-0.0704-0.2159-0.04890.7657-0.08520.5098-0.2874-0.01870.6935-0.19110.597999.108-14.535218.9504
161.26820.36440.4352.7138-0.35921.08810.0138-0.1012-0.0704-0.167-0.02060.01660.0714-0.03290.01280.27610.03350.11480.19310.01950.256543.6971-31.34137.9993
171.69370.0619-0.54050.8369-0.28711.4376-0.00220.43980.0792-0.4734-0.1098-0.43420.06980.20310.1130.67140.06490.18490.44380.08290.452757.282-7.1783-24.2176
181.7458-0.4071-0.34791.24330.10211.289-0.15030.1339-0.1863-0.14370.1383-0.0670.05820.0169-0.01370.3959-0.04150.07660.22210.04110.409155.5728-75.0636-0.5172
191.18070.56560.05071.75440.96971.92470.0565-0.34470.54521.0912-0.24180.1818-0.5640.06960.26390.78390.02450.01560.5076-0.18090.488846.7087-2.857427.0304
201.964-0.0678-0.98580.9750.62621.71550.00120.6570.3141-0.9435-0.11960.16210.1799-0.3054-0.12790.57330.0259-0.01260.43240.12680.458637.8421-12.1789-19.4359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1((chain A and (resid 28:244 or resid 328:369 or resid 451:490)) or (chain E) or (chain F))A28 - 244
2X-RAY DIFFRACTION1((chain A and (resid 28:244 or resid 328:369 or resid 451:490)) or (chain E) or (chain F))A328 - 369
3X-RAY DIFFRACTION1((chain A and (resid 28:244 or resid 328:369 or resid 451:490)) or (chain E) or (chain F))A451 - 490
4X-RAY DIFFRACTION2((chain B and (resid 417:608)))B0
5X-RAY DIFFRACTION3((chain A and (resid 245:327)))A0
6X-RAY DIFFRACTION4((chain A and (resid 370:450)))A0
7X-RAY DIFFRACTION5((chain A and (resid 10:27)) or (chain B and (resid 609:638)))A0
8X-RAY DIFFRACTION6((chain C and (resid 28:244 or resid 328:369 or resid 451:491)))C28 - 244
9X-RAY DIFFRACTION6((chain C and (resid 28:244 or resid 328:369 or resid 451:491)))C328 - 369
10X-RAY DIFFRACTION6((chain C and (resid 28:244 or resid 328:369 or resid 451:491)))C451 - 491
11X-RAY DIFFRACTION7((chain D and (resid 417:608)))D0
12X-RAY DIFFRACTION8((chain C and (resid 375:450)))C0
13X-RAY DIFFRACTION9((chain C and (resid 245:327)))C0
14X-RAY DIFFRACTION10((chain C and (resid 10:27)) or (chain D and (resid 609:637)))C0
15X-RAY DIFFRACTION11((chain R and (resid 28:244 or resid 328:369 or resid 451:490)) or (chain V) or (chain W))R28 - 244
16X-RAY DIFFRACTION11((chain R and (resid 28:244 or resid 328:369 or resid 451:490)) or (chain V) or (chain W))R328 - 369
17X-RAY DIFFRACTION11((chain R and (resid 28:244 or resid 328:369 or resid 451:490)) or (chain V) or (chain W))R451 - 490
18X-RAY DIFFRACTION12((chain S and (resid 417:608)))S0
19X-RAY DIFFRACTION13((chain R and (resid 375:450)))R0
20X-RAY DIFFRACTION14((chain R and (resid 245:327)))R0
21X-RAY DIFFRACTION15((chain R and (resid 11:27)) or (chain S and (resid 609:637)))R0
22X-RAY DIFFRACTION16((chain T and (resid 28:244 or resid 328:369 or resid 451:490)))T28 - 244
23X-RAY DIFFRACTION16((chain T and (resid 28:244 or resid 328:369 or resid 451:490)))T328 - 369
24X-RAY DIFFRACTION16((chain T and (resid 28:244 or resid 328:369 or resid 451:490)))T451 - 490
25X-RAY DIFFRACTION17((chain U and (resid 417:608)))U0
26X-RAY DIFFRACTION18((chain T and (resid 375:450)))T0
27X-RAY DIFFRACTION19((chain T and (resid 245:327)))T0
28X-RAY DIFFRACTION20((chain T and (resid 10:27)) or (chain U and (resid 609:637)))T0

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